- Research article
- Open Access
Neurotrophin/Trk receptor signaling mediates C/EBPα, -β and NeuroD recruitment to immediate-early gene promoters in neuronal cells and requires C/EBPs to induce immediate-early gene transcription
- Anna Maria Calella†1, 3,
- Claus Nerlov†1,
- Rodolphe G Lopez1,
- Carla Sciarretta1,
- Oliver von Bohlen und Halbach2,
- Oksana Bereshchenko1 and
- Liliana Minichiello1Email author
© Calella et al; licensee BioMed Central Ltd. 2007
- Received: 07 October 2006
- Accepted: 25 January 2007
- Published: 25 January 2007
Extracellular signaling through receptors for neurotrophins mediates diverse neuronal functions, including survival, migration and differentiation in the central nervous system, but the transcriptional targets and regulators that mediate these diverse neurotrophin functions are not well understood.
We have identified the immediate-early (IE) genes Fos, Egr1 and Egr2 as transcriptional targets of brain derived neurotrophic factor (BDNF)/TrkB signaling in primary cortical neurons, and show that the Fos serum response element area responds to BDNF/TrkB in a manner dependent on a combined C/EBP-Ebox element. The Egr1 and Egr2 promoters contain homologous regulatory elements. We found that C/EBPα/β and NeuroD formed complexes in vitro and in vivo, and were recruited to all three homologous promoter regions. C/EBPα and NeuroD co-operatively activated the Fos promoter in transfection assays. Genetic depletion of Trk receptors led to impaired recruitment of C/EBPs and NeuroD in vivo, and elimination of Cebpa and Cebpb alleles reduced BDNF induction of Fos, Egr1 and Egr2 in primary neurons. Finally, defective differentiation of cortical dendrites, as measured by MAP2 staining, was observed in both compound Cebp and Ntrk knockout mice.
We here identify three IE genes as targets for BDNF/TrkB signaling, show that C/EBPα and -β are recruited along with NeuroD to target promoters, and that C/EBPs are essential mediators of Trk signaling in cortical neurons. We show also that C/EBPs and Trks are required for cortical dendrite differentiation, consistent with Trks regulating dendritic differentiation via a C/EBP-dependent mechanism. Finally, this study indicates that BDNF induction of IE genes important for neuronal function depends on transcription factors (C/EBP, NeuroD) up-regulated during neuronal development, thereby coupling the functional competence of the neuronal cells to their differentiation.
- Glial Fibrillary Acidic Protein
- Brain Derive Neurotrophic Factor
- Additional Data File
- Primary Cortical Neuron
- Tandem Affinity Purification
The influence of growth factors, as well as transcription factors, on cell fate determination and differentiation is well established. Brain derived neurotrophic factor (BDNF) affects neuronal cortical development by signaling through its cognate tyrosine kinase receptor, TrkB. Together they regulate many cellular functions during and after the development of the nervous system [1–4]. In particular, we have reported that TrkB, via the activation of the Ras/Mitogen activated protein kinase (MAPK) and Phosphatidylinositol-3 kinase/cellular homolog of the viral oncogene v-Akt (PI3K/AKT) pathways, regulates functions throughout the formation of the cerebral cortex, including neuronal dendritic differentiation . While several transcription factors have been found to respond to activation of TrkB and other Trk family receptors, it is not well understood how Trk signaling interacts with the transcription factors regulating neuronal differentiation to activate specific target genes required during the different phases of neuronal development and, subsequently, in neuronal function.
The neurogenic basic helix-loop-helix (bHLH) transcription factors have been shown to be important intrinsic regulators of neural fate determination and differentiation. There are at least two categories of bHLH transcription factors that mediate neurogenesis: proneural bHLHs (Neurogenins and Mash family proteins), which are involved in initiating neurogenesis, and neuronal differentiation factors (members of the NeuroD/Nex family), which are important for terminal differentiation. Studies in mice lacking NeuroD/Nex family members indicate that they are required not only for the survival of early differentiating granule neurons in the hippocampus and cerebellum, but also for their terminal differentiation [6, 7]. Specifically, NeuroD selectively promotes dendrite, but not axonal, morphogenesis in granule neurons through its phosphorylation at distinct sites by CamKII . These factors form heterodimers with ubiquitously expressed bHLH proteins, such as E12 and E47, and activate gene expression programs through interaction, via their basic domain, with DNA sequences containing the core hexanucleotide motif CANNTG, known as the Ebox [9, 10]. It is still unknown which extracellular signals or intracellular mechanisms are involved in the regulation of bHLH factor function.
The CCAAT/enhancer binding protein (C/EBP) family of transcription factors couples growth factor signal transduction with numerous cellular responses, including cellular differentiation in a variety of non-neuronal tissues [11, 12]. The expression of C/EBPs has also been found to change during a number of physiological and pathophysiological conditions in response to extracellular signals, such as hormones, mitogens, and cytokines . Recently, a Mitogen and extracellular signal regulated kinase (MEK)-C/EBP signaling cascade has been implicated in the commitment of progenitor cells toward a neuronal fate in vitro through the inhibition of either MEK or C/EBPs using dominant negative forms . Paquin et al. , using in utero electroporation to manipulate cortical precursors, have suggested that MEK-mediated phosphorylation of C/EBPs is essential for neuronal fate determination. Thus far, however, no genetic model has demonstrated an effect for MEK1/2 or C/EBPs on neuronal lineage commitment or differentiation.
We here identify Fos, Egr1 and Egr2 as genes that are regulated by BDNF/TrkB in a C/EBP-dependent manner. We identify a novel complex between C/EBPα/β and NeuroD, and find that in vivo, these factors are recruited to the Fos, Egr1 and Egr2 promoters in a Trk-dependent manner. Genetic C/EBP depletion leads to a cortical dendritic neuronal differentiation defect, reminiscent of that seen in the absence of multiple TrkB/C alleles, consistent with the idea that Trk signaling through C/EBP-NeuroD complexes mediates terminal cortical neuronal differentiation in vivo.
BDNF induces Egr1, Egr2 and Fos expression in primary cortical neurons
A combined C/EBP site-E-box mediates Fos induction by BDNF
C/EBPs and NeuroD are recruited to IE gene promoters in vivo
C/EBPs mediate BDNF induction of IE genes in primary cortical neurons
Trk signaling regulates promoter recruitment
C/EBPα and NeuroD form a complex in vitro and in vivo
C/EBP depletion leads to defective cortical dendritic differentiation in vivo
The identification of transcriptional targets for signaling by neurotrophin receptors is fundamental to understanding the effects of neurotrophins on neuronal gene expression, differentiation and function. We here provide evidence that, in neuronal cells, C/EBPα and -β form a complex with NeuroD, and that these factors are recruited to the BDNF responsive Fos, Egr1 and Egr2 promoters in a manner dependent on Trk receptor signaling in vivo. Reducing the levels of C/EBPα and -β led to reduced Fos, Egr1 and Egr2 expression in response to BDNF in primary neuronal cultures, and to impaired terminal dendritic differentiation revealed by decreased levels of MAP2 in cortical dendrites in vivo. Together, these results identify NeuroD-C/EBP complexes as mediators of Trk signaling, and identify the IE genes Fos, Egr1 and Egr2 as downstream targets for this pathway.
Nuclear mediators of neurotrophin signaling
Neurotrophins have multiple functions during CNS development, and mediate neuronal survival, migration, differentiation and function. These processes require activation of specific downstream targets. For example, the PI3 kinase-AKT-Foxo pathway is important for neuronal survival downstream of growth factor-induced signaling , and both PI3 kinase-AKT and MAPK pathways are involved in similar functions downstream of TrkB receptor-induced signaling in vivo [15, 23] whereas the phospholipase Cγ (PLCγ)-CamK-CREB pathway regulates hippocampal plasticity downstream of TrkB . Cebpb has been previously shown to be a neuronal transcriptional target downstream of the nerve growth factor (NGF) receptor (TrkA) in PC12 cells . Evidence exists indicating that NeuroD is responsive to neurotrophin signaling in vivo. NeuroD is highly expressed in different tissues, including the developing neurons of the peripheral nervous system (PNS) and CNS, reaching its highest expression during differentiation in the cerebral cortex . In the PNS, NeuroD is required for survival and differentiation of inner ear sensory neurons during later stages [26, 27]. The loss of these sensory neurons in the vestibular-cochlear ganglia (VCG) of neuroD null mice resembles the phenotypes found in mice lacking the receptors TrkB or TrkC (reviewed in ). Moreover, the expression of trkB or trkC in the VCG of neuroD null mice was significantly reduced, , supporting a link between NeuroD and TrkB/C in the survival of newly differentiating inner ear sensory neurons. Similarly, dentate granule neurons of the CNS fail to mature in neuroD/nex1 double mutant mice, indicating that these molecules are critical not only for the survival of early differentiating neurons, but also for their terminal differentiation [29, 30]. Although no such phenotype was observed in the neocortex of neuroD/nex1 animals, this may be explained by NeuroD family members being functionally redundant.
We have identified NeuroD-C/EBP complexes as novel mediators of Trk signaling in vivo. The finding that inhibition of these complexes (through deletion of Cebpa and Cebpb alleles) has effects on cortical differentiation similar to those seen by reduction of Trk signaling during development (through disruption of Ntrk2 and Ntrk3 alleles; supplemental Figure 4 in Additional data file 1, and previous work in which we have shown that TrkB/C cooperate in promoting the survival of differentiating hippocampal and cerebellar granule neurons , and that TrkB regulates functions throughout the formation of the cerebral cortex, including dendrite neuronal differentiation ) is, furthermore, consistent with Trk signaling through NeuroD-C/EBP being required for MAP2 induction and dendrite growth. Given that C/EBPs and NeuroD are induced during neuronal lineage commitment in vitro, it is interesting to speculate that their appearance allows Trk receptor signaling to regulate genes involved in subsequent terminal neuronal differentiation and function.
Of the targets found to be affected in this study, Fos and Egr1 have both been implicated in dendrite formation in PC12 cells [31, 32]. Genetic ablation of Fos, Egr1 or Egr2 has not been reported to affect dendrite differentiation in vivo, suggesting that the combined downregulation of multiple targets leads to the observed effects on neuronal dendrite differentiation. It is, however, equally possible that some of the NeuroD-C/EBP targets are involved in neuronal function, since Egr1 has been reported to be required in the CNS for long-term synaptic plasticity (LTP) in the dentate gyrus . The known functions of the affected genes are, therefore, consistent with the observed differentiation phenotype, and suggest a role for C/EBPs in the generation of LTP. However, given the possibility of functional redundancies, further genetic analysis will be required to resolve this issue.
We did not observe any effects of C/EBP depletion on gross CNS morphology or the distribution or number of neurons and glial cells, as determined by histological analysis and quantification of NeuN and GFAP. Previous reports [13, 14] have shown that high levels of dominant-negative C/EBP were able to inhibit neurogenesis. Our genetic data do not, at this point, confirm a role for C/EBPs in neuronal-glial lineage decisions. However, in addition to C/EBPα and β, C/EBPδ and ε are also expressed in the CNS and may be able to compensate for loss of the α and β isoforms. In addition, due to the early embryonic lethality of mice lacking all Cebpa and Cebpb alleles, one wild-type allele was intact in our analysis, which may be sufficient for any commitment step. It should be noted that the use of high levels of dominant negative C/EBPs may affect other related transcription factors (such as C/ATF and CREB/CREM), and confirmation of the proposed C/EBP function in neuronal lineage commitment by genetic means will still be important to finally resolve this issue.
Recruitment of C/EBP-NeuroD complexes to target promoters
The promoter elements in the Fos, Egr1 and Egr2 promoters that recruit C/EBPα/β and NeuroD have significant homology, but in the case of Egr1 and Egr2 do not contain a consensus Ebox. This raises the possibility that the C/EBP-NeuroD complexes that form in vivo in neuronal cells expressing these factors (as determined by TAP-mediated pull down from mouse forebrain tissue) are recruited through a single binding site for C/EBP, with little or no interaction between NeuroD and DNA. This notion is supported by the observation that mutation of the Fos promoter Ebox had no effect on Fos promoter activity in transient transfection assays, whereas simultaneous mutation of both the C/EBP site and the Ebox significantly decreased promoter induction by BDNF.
The recruitment of NeuroD and C/EBPα/β to IE gene promoters was impaired in vivo when the levels of Trk signaling were decreased by inactivation of Ntrk2/Ntrk3. This result demonstrates that Trk-mediated signaling regulates the association of these factors with chromatin, and the observation that NeuroD and C/EBP recruitment were highly correlated is consistent with these factors being recruited as a complex, as discussed above. Importantly, lowering the level of C/EBP through Cebpa/Cebpb inactivation decreased the inducibility of all three IE gene promoters in response to BDNF, providing a direct link between the level of C/EBP (and by inference C/EBP-NeuroD complexes) available and neurotrophin-mediated gene activation. While C/EBPs, therefore, are an essential component of TrkB/TrkC mediated IE gene activation, the events linking Trk signaling to C/EBP and/or NeuroD remain to be fully understood at this point. Both C/EBPs and NeuroD are known to be phosphorylated in response to extracellular signaling; however, the physiological relevance of these phosphorylation events are yet to be addressed genetically. Perhaps most relevantly, from in vitro studies, phosphorylation of C/EBPβ Thr188 by ERK, and Thr217 by ribosomal S6 kinase (Rsk), both of which are kinases downstream of MEK , have been proposed to be required for their role in neuronal lineage commitment [13, 14]. We find that Trk-mediated IE gene induction depends on the Shc adaptor-binding site, a principal function of which is to mediate high-level sustained ERK activation in cultured neurons . It is therefore possible that, also in the context of a NeuroD-C/EBP complex, this pathway regulates C/EBP activity. Experiments to address this question genetically are currently underway.
In summary, we have shown here that C/EBPα and NeuroD form complexes in vivo and in vit ro. These may define a novel class of C/EBP-bHLH transcription factor complexes of widespread importance, as we have recently shown that a similar interaction occurs between C/EBPα and SREBP-1 in hepatocytes . ChIP analysis and genetic depletion demonstrated that recruitment of C/EBP and NeuroD to IE gene promoter chromatin occurred concurrently in a Trk-dependent manner, and was required for IE gene induction by neurotrophins. The physiological result of C/EBP depletion was reduced MAP2 expression and impaired cortical dendritic differentiation. We have, therefore, identified C/EBP-NeuroD complexes as novel mediators of Trk signaling, and provide evidence that such complexes function in late stages of neuronal development to promote terminal neuronal differentiation.
RNA preparation for microarray analysis and RT-PCR
Primer sequences used for RT-PCR, q PCR and ChIP
3' UTR Fos
The constructs pMSRF/cebp, pMcebp/ebox, and pMebox were created as previously described . Mutations in the pMSRF/cebp and pMcebp/ebox constructs were introduced as described , whereas for the pMebox construct the QuickChange Site-directed Mutagenesis Kit was used (Stratagene, Milan, Italy). The oligonucleotide primers used to generate pMSRF/cebp, pMcebp/ebox and pMebox constructs carried the following mutations (underlined), respectively: tgtccatcgg aggacatctgcgtcagcaggtttccacggcc, tgtccatattaggaacg ctgcgtcagcaggtttccacggcc, and tgtccatattaggaa atctgcgtcagcaggtttccacggcc. C/EBPα was introduced as Bam HI-Eco RI fragments in pcDNAI (Invitrogen, Milan, Italy) for in vitro labeling , and in pcDNA3.1 (Invitrogen) for transfection. Mouse NeuroD full-length cDNA was obtained by RT-PCR using RNA isolated from cortical neurons and the primers Bam HI/5'-cgggatccgtggaaacatgacc-3' and 5'-ggaattcactgacgtgcctcta-3'/Eco RI.
Cultures of cortical progenitors and postmitotic neurons
Cortical progenitors, as well as postmitotic neurons, from mouse embryos were cultured according to previously described methods [15, 39]. Briefly, cortices were collected from E12-13 mouse embryos, triturated, and then plated on poly-L-lysine (at different densities depending on the final experiment). The culture medium consisted of Neurobasal medium (GIBCO BRL (now Invitrogen), Milan, Italy), 0.5 mM glutamine, penicillin-streptomycin, 1% N2 supplement (GIBCO BRL), and basic fibroblast growth factor (bFGF) (40 ng/ml; R&D Systems, Milan, Italy). After 48 hours, medium was replaced with the same medium containing 2% B27 supplement (GIBCO BRL) instead of 1% N2 supplement. Postmitotic neurons were prepared from cerebral cortices of E15.5 mouse embryos derived from crosses of wild-type or trkBSHC/SHChomozygous mice. Cortical neurons were cultured and BDNF stimulated as described . Purified recombinant BDNF (Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA) was added to the culture medium at a concentration of either 5 or 50 ng/ml, as indicated.
Cortical progenitors after either 1 or 4 days in vitro (DIV) were fixed in 4% paraformaldehyde (PFA) for 20 minutes. Washes were performed with 10 mM phosphate-buffered saline (PBS)/glycine to neutralize the PFA. The cells were permeabilized with 0.5% NP-40/PBS for 5 minutes. Blocking solution was added for 1 hour (10% NHS, 0.3% Carrageenan Lambda (Sigma, Milan, Italy), 0.5% TritonX100 in 50 mM TBS) at room temperature, followed by incubation with either a mouse monoclonal anti-MAP2 antibody (1:300, clone AP20, ChemiconMilan, Italy) or a mouse monoclonal anti-Nestin antibody (1:300, clone 401, Chemicon) in 1% normal horse serum (NHS), 0.3% Carrageenan Lambda, 0.5% TritonX100, 50 mM Tris-buffered saline (TBS), O/N at 4°C. Immunostainings were visualized using a fluorescein-conjugated goat anti-mouse IgG (H+L) (1:200 in TBS, Jackson IR, Milan, Italy). The slides were mounted with Vectashield mounting medium (Vector H2000, Milan, Italy).
Transfection of cortical neurons and luciferase assay
Cortical neurons were plated at 3 × 106 cells per 60 mm well. Transfections were carried out on either 3 or 4DIV using Lipofectamine 2000 reagent (Invitrogen) according to the manufacturer's protocol. Briefly, one 60 mm well of cells was transfected with 2.3 μg of reporter plasmid plus 3 μg of the plasmid ras sarcoma virus long terminal repeat containing the Escherichia coli beta-galactosidase gene (pRSV-β-gal). Then, 24 hours after transfection, cells were left unstimulated or stimulated with 50 ng/ml of BDNF for 2 hours. Cells were then lysed in 250 μl of Triton lysis buffer (100 mM potassium phosphate pH 7.8, 0.2% Triton X-100, 1 mM dithiothreitol (DTT)). Cell debris was removed by centrifugation, and the lysates were used in luciferase and β-gal assays. The luciferase activity was measured using a Lumat LB 9507 luminometer (Berthold Technologies Wildbad, Germany). The fold induction was defined as the ratio of β-gal normalized luciferase activity in lysates of stimulated cells relative to the normalized luciferase activity from unstimulated cells.
Plasmids used for cotransfections included pcDNA3.1 (Invitrogen) driving the expression of C/EBPα or NeuroD, and a wild type (pWT) or mutated (pMcebp/ebox) Fos promoter driving expression of luciferase. NIH3T3 cells were grown to 60% to 80% confluence in 30 mm wells and transfected with a total of 1.5 μg of DNA including 250 ng of the luciferase reporter plasmid and 250 ng of pRSV-β-gal plasmid for normalization. Cells were transfected using FuGENE 6 (Roche) according to the manufacturer's protocol. After 24 hours, cells were harvested, lysed, and the β-galactosidase and luciferase activities were measured as described above.
Co-immunoprecipitation assay and western analysis
pCMV-Tag3 vector (Stratagene, Milan, Italy) was used to express NeuroD possesssing one Myc-epitope tag, and pcDNA3.1 (Invitrogen) was used to express C/EBPα possessing one Flag-epitope tag. Q2bn cells were grown in DMEM supplemented with 8% fetal bovine serum and 2% chicken serum, transfected using calcium phosphate, and harvested 24 hours after transfection. Cells were disrupted in lysis buffer (50 mM Tris pH 7.4, 1.5 mM MgCl2, 100 mM NaCl, 0.5% Triton X-100) supplemented with a protease inhibitor cocktail (Roche) on ice for 15 minutes, and then incubated at room temperature for 30 minutes with 0.25 u/μl of benzonase (Sigma). After clarification by centrifugation, lysates were subjected to Co-IP using 20 μl of anti-Flag M2 affinity gel beads (Sigma) at 4°C overnight (O/N). The beads were collected and washed, and the bound proteins were eluted by a competition with 3X FLAG peptide (Sigma), and analyzed by SDS-PAGE followed by western blotting using anti-Myc tag antibody (1:2000, Ab9106, Abcam, Cambridge, UK) and anti-Flag tag antibody (1:2500, Sigma). Analysis of pERK1/2 and pAKT in stimulated cortical neurons derived from cerebral cortices of E12.5 mouse embryos of controls and different Cebpa and Cebpb mutants was carried out using western blots as described . The monoclonal anti-pERK1/2 antibody was used at 1:2000 (clone E10, New England Biolabs, Frankfurt, Germany), the rabbit polyclonal anti-pAKT (Ser473) was used at 1:1000 (Cell Signaling, Frankfurt, Germany), and the monoclonal anti-α-tubulin antibody was used at 1:20.000 (clone DM1A, Sigma).
GST pull down assay
The GST fusions C/EBPβ bZIP (amino acids 231 to 328 of chicken C/EBPβ) and C/EBPα bZIP (amino acids 256 to 358 of rat C/EBPα) were constructed by PCR amplification and cloning into pGEX4T-1 (Pharmacia, Milan, Italy). GST C/EBPα TAD (amino acids 1 to 96) has been described . 35S-labeled NeuroD was prepared using the Promega TNT T7 system and L-35S-methionine (Amersham Biosciences) according to the manufacturer's suggestions. Pull down experiments were carried out by pre-incubating 100 μl of bead suspension (corresponding to about 500 ng protein) with 50 μl 10% bovine serum albumin (BSA) and 350 μl pull down buffer (50 mM Tris pH 8, 250 mM NaCl, 0.5% NP40) for 30 minutes at room temperature with gentle shaking. 35S-labeled protein (5 μl) was subsequently added, and the incubation was continued for 1 hour. The beads were then washed 3 times with ice-cold NETN buffer (0.1 M NaCl, 1 mM EDTA, 10 mM Tris pH 8.0, 0.5% NP40), pelleted, and resuspended in 20 μl of 2X SDS buffer (20% glycerol, 4% SDS, 10% β-mercaptoethanol, 125 mM Tris-Cl pH 6.8, 0.2% bromophenol blue). The samples were boiled for 5 minutes, and the beads were pelleted. The supernatants were resolved by SDS-PAGE (12.5%). Labeled proteins were detected on a Fuji BAS2040 phosphorimager (Milan, Italy).
Tandem affinity purification
Wild-type (+/+) and CebpaTAP/+(T/+) E16.5 forebrains were dissected, and then lysed in hypotonic buffer (25 mM Tris pH 7.4, 50 mM KCl, 2 mM MgCl2, 1 mM EDTA, 1 mM DTT, protease inhibitors from Sigma) for 20 minutes on ice. The samples were centrifuged at 4,000 rpm for 20 minutes at 4°C to collect the nuclei, which were washed in hypotonic buffer and resuspended in benzonase buffer (50 mM Tris pH 7.4, 1.5 mM MgCl2, 100 mM NaCl, 10% glycerol and 1 mM DTT and protease inhibitors). Benzonase (Novagen, Milan, Italy) was then added at 0.25 u/μl and left at room temperature for 25 minutes, after which lysates were supplemented with 0.2% NP40 and left on ice for 10 minutes. The nuclear extracts were collected by centrifugation at 14,000 rpm at 4°C for 20 minutes, and 5 mg of this were used in IP after a pre-clearing step with proteinA sepharose beads (Pharmacia) at 4°C for 30 minutes. We added 20 μl rabbit IgG agarose beads (Sigma) to the extracts and incubated them with gentle rocking at 4°C for 2 hours. The beads were washed three times with lysis buffer followed by TEV protease buffer (10 mM Hepes-KOH pH 8.0, 150 mM NaCl, 0.1% NP-40, 0.5 mM EDTA, 1 mM DTT). TEV protease (Invitrogen) was then added at 0.3 u/μl and left overnight at 4°C. Proteins in the supernatant of centrifuged samples were precipitated using acetone, dissolved in 20 μl of sample buffer, and loaded on a 10% SDS-PAGE gel. Western blot analysis was performed using an anti-NeuroD antibody (1:500; D-20, SantaCruz, Milan, Italy) in 5% BSA. Stripped membranes were re-probed with an anti-C/EBPα antibody (1:500; 14AA, SantaCruz).
ChIP assays were performed essentially as previously described . E16.5 or P0 wild-type mouse forebrains were quickly dissected, cut into small pieces, and incubated for 10 minutes in 1% PFA at 37°C. The tissues were collected, washed in PBS, and resuspended in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1) containing 1 mM phenylmethylsulphonyl fluoride (PMSF) and 2 mg/ml aprotinin. After sonication, lysates were cleared by centrifugation and diluted 10-fold with dilution buffer (0.01% SDS, 1% Triton 100X, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 150 mM NaCl). After a preclearing step using a salmon sperm DNA/ProteinA agarose slurry (50% slurry, Upstate, Milan, Italy), the chromatin was incubated O/N at 4°C with either rabbit Ig, or 2 μl of C/EBPα (14AA, SantaCruz), C/EBPβ (#3082 polyclonal, Cell Signaling), NeuroD (Santa Cruz), histone H3 (Abcam), or acetylated histone H3 (Upstate) antibodies. IP complexes were collected using protein A/G sepharose beads, and washed twice with dilution buffer, once with 500 mM NaCl, and once with Tris-EDTA buffer. After the final wash, 250 μl of elution buffer (1% SDS, 0.1 M NaHCO3) was added, and the beads were rotated at room temperature for 15 minutes. The elute was supplemented with 5 M NaCl and incubated for 4 hours at 65°C to reverse the formaldehyde cross-linking. To analyze the DNA, samples were treated with 40 ng/μl of proteinase K (Merck, Milan, Italy) for 1 hour at 45°C, extracted with phenol:chloroform, and ethanol-precipitated in the presence of glycogen as carrier. The final IP DNA products were resuspended in 20 μl of 10 mM Tris-HCl and 1 mM EDTA, of which 2 μl was used for PCR analysis with 50 pmol of each primer (Table 1) in a final volume of 50 μl.
qPCR or qRT-PCR was performed using the DyNAmoSYBR Green qPCR kit according to the manufacturer's protocol (Finnzymes, Milan, Italy) using the primers indicated in Table 1. For the ChIP, serial dilutions of IP DNA were subjected to real time PCR. After running the qPCR reactions, crossing threshold (Tc) values were determined for each sample. The Tc value was defined as the cycle at which the fluorescence rises above a baseline threshold, using iCycler software (MJ Research, Cambridge, MA). To normalize for variations in the amount of starting DNA, a ΔTc value was calculated by subtracting the Tc value for the immunoprecipitated sample from the Tc value for the corresponding input DNA. DNA quantities were then expressed as percentages of corresponding input using the ChIP sample as a percentage of input = 2Δ(Tc) × 100. Only when IP samples contained > 1.5 times as much DNA as the Ig samples were they considered to have sufficient DNA for analysis .
Transgenic mouse strains
The methods used to generate the knockouts of trkB, trkC, and trkB SHC have been previously described [15, 17], as well as those used to generate the knockouts of Cebpa (generously provided by Drs D Tenen (Harvard University, Boston MA, USA) and G Darlington (Baylor College of Medicine, Houston TX, USA) and Cebpb (generously provided by Drs PF Johnson and E Sterneck (National Cancer Institute, Bethesda DC, USA), the floxed Cebpa ( generously provided by Dr YH Lee, Institute of Molecular Biology, Accademia Sinica, Taipei, Taiwan), and the transgenic NestinCre mouse lines [5, 19, 20, 43]. The C/EBPα-C-TAP strain was generated according to  (O Ermakova and C Nerlov, unpublished data).
Histology and protein expression levels
Histological and immunohistochemical (IHC) analyses were carried out as described previously . Brain tissue biochemistry was performed as described . The specific antibodies used to evaluate neuronal differentiation were NeuN (1:500 WB, 1:100 IHC, clone A60, Chemicon), βIII-tubulin (1:10,000, clone Tuj.1, AbCam), GFAP (H-50; 1:500, polyclonal, Santa Cruz), MAP2 (1:300, clone AP20, Chemicon) and NF68 (AB1983; 1:250, polyclonal, Chemicon). The antibodies anti-PLCγ-1 (1:2,000, mixed monoclonal, Upstate), anti-Erk1 (1:3,000, monoclonal, Zymed, Milan, Italy), and anti-α-tubulin (1:20,000, clone DM1A, Sigma) were used to control for protein loading. For the analysis of NeuroD protein expression, P0 cortices from Cebpa/b and trkB/C mutants and controls were lysed in (50 mM Tris pH 7.4, 1.5 mM MgCl2, 100 mM NaCl, 0.5% Triton X-100) supplemented with a protease inhibitor cocktail (Roche) on ice for 15 minutes, and then incubated at room temperature for 30 minutes with 0.25 u/μl of benzonase (Sigma). Western blot analysis was performed using an anti-NeuroD antibody (1:500, D-20, SantaCruz) in 5% BSA. Stripped membranes were re-probed with an anti-SP3 antibody (D-20X; 1:1,000, polyclonal, SantaCruz). Densitometric analysis  of imaged blots was used to compare the expression levels of proteins in mutant and control brains, and was performed on three different blots for each antibody. The ratios obtained for mutant and control samples were compared statistically using Student's t-test.
Golgi method and analysis of dendritic thickness
Mice were perfused with 4% PFA in phosphate buffer. Brains were dissected and post-fixed in 4% PFA. Golgi staining was performed according to the Golgi-Kopsch method, as described previously . Briefly, blocks of brain tissue (approximately 2.5 mm thickness) were prepared and soaked in a solution containing 2.5% potassium-dichromate for 1 day at room temperature in the dark. The solution was then replaced with fresh of 2.5% potassium-dichromate solution, and tissues were incubated for another 6 days. Tissues were then washed and transferred to a solution containing 0.75% AgNO3. After 5 to 6 days, brain pieces were removed, washed in 40% and 20% ethanol, and cut into 80 μm coronal sections using a vibratom (Leica, Heidelberg, Germany). Sections were mounted on gelatin-coated slides and coverslipped with Merkoglas (Merk, Darmstadt, Germany). Analysis of dendritic thickness was performed on Golgi-impregnated sections that were uniformly dark throughout the section. Only dendrites that displayed no breaks in their staining, and were not masked by other neurons or artifacts, were evaluated. Quantitative three-dimensional analyses were performed using a combined hardware-software system (NeuroLucida, Microbrightfields Inc., Colchester, VT, USA) controlling the x-y-z axis of the microscope (Axioscop Imaging, Zeiss, Rehlingen, Germany), and a microscope-mounted video camera (Hitachi, Tokyo, Japan). The three-dimensional reconstruction was done using a 100× objective (NA: 1.4; oil immersion) and the NeuroLucida system. Mean dendritic thickness was calculated from the reconstructed dendrites with the help of NeuroExplorer (Microbrightfields Inc.). The mean, standard deviation (SD), and standard error of the mean (SEM) were calculated. ANOVA followed by a Newman-Keuls test were used for statistical analysis, and were performed using Prism 4.0 (Graph Pad, San Diego, USA).
Authorization for the use of experimental animals
The EMBL-Monterotondo Animal Ethics Committee approved all animal procedures. We further confirm that all animal experiments conformed to Italian and European regulatory standards.
We wish to thank Dr E Reuvni for the promoter sequence analysis, and E Perlas for excellent technical assistance, and Regeneron Pharmaceutical Inc. for providing recombinant BDNF. This study was supported in part by a grant from the European Union (EuroStemCell) to LM and CN. OvBuH was supported by the Deutsche Forschungsgemeinschaft (SFB 636/A5).
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